The Big Apple Goes Small
by TheDevilsDen
Summary: A young man named Alex Mercer gets infected by himslef. He fights his way with Percy Jackson, through the military to find out that the Greek Gods are real. While the Gods watch him, he finds himself not only at the center of the military but Greek myths as well.lol terrible Im am terrible at summaries.
1. Boys and There Ways

Percy Jackson Prototype Crossover

I do not own PJO, Rick Riordon does :D

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><p>My name is Percy Jackson. Some call me a terrorist, some call me a murderer, and some call me a monster. I am all of those things. Every day more people get infected. I'm the cause of it. If Gentek wouldn't have tried to find out what the infection was made of then I would have been a normal man, but it never works out like that. Oh no, it never does. See my life is full of pain and hunger for revenge. I want to find out about my past, and when I do I will have my revenge.<p>

I am the PROTOTYPE.

Chapter 1, THE PROTOTYPE IS MADE

It has been two days since I was infected. I was in Penn Station and, ugh I can't remember. Anyway me and my friend Grover were sitting in the second to last seat in our school bus. Grover knew about me getting infected and kept trying to cheer me up, but it's hard to cheer up right after you got infected by your own infection. As we rode we had to put up with Nicole Rose, a red head kleptomaniac girl who kept hitting Grover with a peanut butter and mayonnaise sandwich. I would have killed her right then and there by grabbing her and consuming her. She would always make fun of me because she saw me when I was lying down looking like I was dead when I wasn't when I got infected.

The military has the entire island of Manhattan on a plague lockdown. Which means nobody goes in, nobody comes out. Maybe that will change one day. Maybe.

My parents and close friends only know my real name no one else. Not even the military. My "code" name is Alex Mercer. If I were to ever reveal my powers to anyone then the military would be on my ass.

"Alex," teased Nicole,"your face looks stupider than when you got half killed."

At that my heart got faster, my arms got tighter, and my brain short circuited. I screamed and somehow tentacles came out of my body and made the bus explode. She, Grover, and I flew out unharmed, but the others weren't so lucky. They were stabbed by the tentacles and fell down. They were almost dead. I was... I don't know what I am, or anything about my past, and why do I care about these people? They are the ones that tease me about my past. It seems they know more about me than I do.

My teacher, , looked at me in a look that said, _You are special._ was always like a wolf. She would tell you what was done wrong and what was done right, like a mom teaching her pups.

OoOoOoOoOoOoOoOoOoOoOoOOoO

I ran. I ran as fast as I could, but I couldn't get away. The stupid military has helicopters, tanks, and Strike Teams. They would corner me, but I'd break through the wall and get away. Only for a good long ten minuets. Then they would find me.


	2. The Meeting of the Men

**Hi guys/girls, sorry I haven't updated in such a long time, and anyways thanks for the reviews. Trust me when I say Prototype will keep you feeling like a badass the entire way through the game… I don't own PJO or Prototype. But thanks for the reviews. Don't worry I plan to make the PJO part sort of near the end so I can add the Titan War with the boss fight of Prototype. I will add some PJO at the start so I can spice it up a little! And in the game Prototype you can run up the sides of buildings, and I'm doing Prototype 1 not 2.**

Chapter 2, Alex

**(AN/ The first chapter was a prologue/sort of epilogue. You guys/girls will understand when you play Prototype. Trust me.)**

As I woke I could barely see my surroundings. It was all blurry.

"Give me the 8" blade**(8" means 8 inch)**, we'll start by cutting the torso."

Just then I sat up from my "bed". I took a careful look at my surroundings. I'm in a morgue. A place where they store dead bodies.

"Get the kill team in here now!" I heard someone yell.

I looked up to see two doctors running out the door. I slid off the bed and walked out the door. I turned the corner to see two helicopters hovering to the ground.

"You have to get in there he was dead and now is alive!" I saw the first doctor yell.

"I don't believe you," A soldier said, then shot the doctor. Then another soldier shot the second doctor. That's when I took my chance to run.

"Halt, stop right there!" A soldier yelled.

"Hey wait don't…" I was cut off by them shooting me. I fell down yelling "WHATS HAPPENING TO ME!" Then I looked for a way out. I saw a big, but not too big, wall. I ran at it and jumped at it with all of my might, I guess. I cleared the wall!

"That was easy." I muttered to myself. I looked and saw another wall, and I cleared it too. Then I saw a helicopter. I looked down the street**(AN/ I have been to New York, but not in the city so just bear with me about my navigation skills :D)** and I ran with the helicopter chasing my ass. I ran until the helicopter shot a few rockets at me and a car.

I flew but then held my ground and grabbed the car out of midair and yelled, "WHAT ARE YOU GOING TO THROW AT ME NEXT HUH? WHAT DO YOU WANT FROM ME!"

The helicopter just flew forward and was about to drop a couple men on the ground. I then threw the car at the helicopter and it went down. I saw some glowing red things come out of the helicopter when it crashed. I went to check it out and when I got near it, it sucked right into my body. I was afraid at first but I felt more refreshed, like I ate some espresso jellybeans**(Percy Jackson reference. Anyone… okay.)** and my health came up a little.

I have to get to higher ground, I thought. I looked up at a building and thought, do I take the elevator or do I do something else? Let's try the "something else". I ran as fast as I could and ran up the side of the building. I looked up and thought, I need to get higher. I jumped up on a little water tower and jumped to another building. When I got to the top there were 3 or 4 more helicopters waiting for me. I looked at some air conditioners on the roof of the building and grabbed one and threw it at the first helicopter and it went down with a big bang. The next three helicopters I just decided to kick them down… Literally. I jumped up in the air and kicked them and they went down.

I muttered to myself, "This can't be happening."

MEANWHILE

Percy POV**( Okay in the first chapter it was Percy but I messed up,*spoiler alert for end of my book* Percy wanted to get infected by Alex so he would get Alex's powers.)**

"Hey mom, why is everyone fighting over there?" I asked my mother.

My mom Sally looked out the window and said, "Um, honey they are just practicing."

I knew that she knew I wasn't convinced, but I let it go. (I wish I didn't.)

Later that day I had to go to school. I met up with Grover my best friend. He was a scrawny kid. He cried whenever he got frustrated. He always wore pants. He already had a beard forming on his face. He walked with a funny limp. He got an excuse to never go to P.E. for the rest of his life because he had some sort of muscle disorder in his legs, but don't let that fool you, you should see how he runs when it's enchilada day in the cafeteria.

When we got to school I ran into my dorm and took a shower. Finally I can get the stench off Smelly Gabe off me. Sorry Smelly Gabe is my stepfather. Sorry to say it but he smells like a person's asshole dripped in puke and poop mixed together. No lie. When I got done with my shower I went to get my clothes.

When I got back to my bed they weren't there. I heard giggling and look up to see no one other than Nicole Rose.**(First chapter anyone?) **She and her friends were holding my clothes up in the air. Waving them around like they just don't care. Hey that rhymed.

"Looking for these?" Nicole said trying to act all nice and innocent.

"Yea, now give them back." I tried to snatch them out of the air, but I tripped on my towel and fell to the ground. Nicole and her clan laughed at me. That's when I got mad and everything went black and a wave rushed in my ears. When my vision came back I saw Nicole drenched and lying on the ground. The floor around her was drenched by water.

Nicole looked at me in disgust and screamed, "Percy pushed me!"

Her clan looked at me frightened and ran away screaming. Nicole got a look in her eye, a bad one and said, "Ha now I have witnesses to your bad behavior, Jackson!"

I just went back to my room and got dressed. Right as I was about to leave I heard a scream coming from outside my window. I looked out to see more helicopters fighting one guy who was jumping with major "ups". Just then one helicopter shot him with a missile and he went flying. Flying right into me! He came through my window and crushed me. The guy stood up and looked to be about 20 to 25 years old, thank the Gods I'm sixteen.

He turned to me and said, "Hello child."

"Umm, hi." I responded.

"Please would you tell no one that I'm here?"

I wasn't sure about how to react. I could scream and run, or I could help the guy. I decided to help him.

"Okay I'll help you. On one condition."

"Ask away." He said.

"You will protect me if I'm ever in serious trouble."

"That sounds like the easiest thing ever."

"Yea well you see I have been kicked out of a lot of schools."

"So I've got super powers, I can handle anything."

In a week there will be a war between the Gods and the Titans, I thought, how can he protect me?

"Okay if you come with me I can help you protect me."

"Okay kid I'll be your pet."

We started to walk down the hall when Nicole came around the corner. She walked up to me and kicked me in the gut. The guy looked at her shockingly but regained his focus and kicked her literally about 40ft down the hall.

He looked at me and was about to say something, then thought about it, but asked it anyway, "What is your name kid, I never caught it?"

"My name is Percy Jackson, and what about you sir?"

He looked at me really serious and said, "I'm Alex. Alex Mecer."

OoOOOoooOOOoooOOooOoOOooOOoo

**WOOO I DID IT. Thanks guys/girls for reviewing it really boosted my morale to write this story. Trust me it will get way better when I get my comedy skills up :D. See ya, and have a good day! **


	3. The Goliath

PJO PROTOTYPE crossover part III (3)

**Hey people, I've decided to cut to the chase get to the part about the War. I think it's better if I do that. R&R!**

Alex POV

Today was the day of the war. It wasn't a fun one, but I had fun slicing people in half.

It was rainy when I went with Percy and Nico to the Underworld. On the way there Percy had tried to call Annabeth after pissing her off at camp. Anyway when we were on the stairway of Orpheus, or something, Percy's pet hellhound, , or something, was getting us stuck halfway through, so I had to push her the rest of the way down. It wasn't really that hard, but it was annoying. When we finally got down we headed directly towards The River Styx.

I looked at the polluted river and said, "I wonder what happened to the people who threw these dreams away."

Nico told me to stay where I was and he was going to take Percy somewhere. So I stood there for what seemed like an hour and then I heard the sounds of alarms going off. I looked to Percy running at me with Nico slung over his shoulder. He set Nico down and asked him what he needed to do. Nico sounded drunk but replied something that probably meant, "Just go in the river."

I just waited and watched as Percy tried to act all courageous as he stepped into the river. He fell as soon as his feet hit the water. He was in the water for about thirty seconds then he finally came back up. His skin was burning red.

I asked him, "How do you feel?"

He said, "I felt like I just took a bath in acid 10000 times."

We both laughed at that comment. Then I heard someone yell. I looked over to see Hades and his undead army coming at us. I went into my claw powers and ran at the army. The rest that I didn't destroy shot me with their muskets. Most hit me, but felt like a small tickle. Then I saw Percy hacking his way through the army they shot him but the bullets flecked off like tiny flies on a weedwacker, or whatever the hell it's called. He cut his way right to Hades and jumped on him. The he pinned Hades and I jumped on Hades too, to make sure he didn't escape. I'm sure we could've beaten the hell out of him, but he disappeared right as I was about to gut him with my blade power.

"METAPOD USE HARDEN," I heard Nico yell as he was asleep. He looked like he was Pikachu fighting a little Mudkip**(AN/ I HATE POKEMON. All of my friends are nerds about it…)**.

FASTFORWARD TO BEGINNING OF THE WAR

Alex POV

"So," Kronos said, "You have an infected as your partner Jackson."

Percy sneered at Kronos and said, "At least I have friends."

Kronos flashed me a glare that probably scare a fly, but definitely not me. I glared back and I think I saw his glare waver for a bit, but then it was replaced by his glare again.

We kept glaring until he said, "Well for our first gift shall we give young Alex Mercer the Goliath or the couple dozen Hunters?"

The monsters cheered for the Goliath. Then the battlefield went quiet. Then a huge roar broke through the city.

I looked down the road and saw something that I knew would kill a lot of us if I didn't stop it.

The Goliath.

**Haha. I wanted to do that to cliffy you guys/gals. Don't worry I'll update soon to show you people the Goliath. :D:D:D:D:D:D:D**


	4. The Start of the Real War

**Hey Soooooo sorry for the long wait it's just that school has been killing me with all of the projects that we have to do before school ends. It just nearly made me die of school sickness.**

**Any way on with the story!**

Alex POV

Shit. That's all I need to say about what is happening.**(The Goliath is from prototype 2 but I thought I'd just add it for fun :D)** The thing was massive. Bigger than the apartment of Percy's mother, and stepfather, Paul.

The monster then tried to claw me to the ground, but I dodged it. It's claw was stuck in the ground.

_Hm, I could use that to my advantage, _I thought.

I jumped up and clawed the Goliath's arm off. It wailed in pain, but recovered almost immediately. It then let out a scream that brought a bunch of Hunters**(The monsters from Prototype, not Artemis' Hunters :D)**with it. Then the Goliath brought its giant meaty head down and screamed at everything around it. I then took the chance to claw at its head. I sliced its head about four times before it brought its head back up in pain.

Then the Goliath tried to smash me with its leg. I dodged that as well. Then it lied there, so I took the chance to take out its leg. It let out a wail of pain. Then did something no one could've expected. It thrust itself into the air and tried to smash me with its giant club hand. Everyone, even Kronos, looked at it with fear and amazement. It then flew right back down to the ground, and smashed everything near it to pieces. It missed me, but I knew it had better accuracy than that. It turned to me and jumped up again. I dove out of the way, and the monster laid stunned on the ground.

I then took the chance to claw its head and rip its brains out. I jumped on its brain and consumed the entire Goliath.

Strength coursed through my veins and I felt like I could lift five Goliaths. I looked up at Kronos with my best glare I could make. He looked ready to drop everything and shit his pants while burning in the hottest pits of the Underworld there is. He looked at his companion Titans.

"Well, well. Looks like you need a sit down." He said.

He struck his scythe into the ground and brought out new monsters from the Infection.

"Yes look at them," Kronos said, "These beasts are called Brawlers**(Also from prototype 2)**, they are much more dangerous than the regular Hunter."

I looked at the Brawlers, they didn't look like they wanted to fight me. I looked at one and pointed at Kronos. All of the Brawlers, which were about thirty, turned to Kronos and jumped on him looking for a weak spot. Then Kronos shot a beam of light out of his scythe which killed all of the Brawlers.

He looked at me with a murderous glare which only scared the youngest of the campers fighting the other monsters of the "Greek Mythology". He turned to his army of demons and monsters, and yelled a war cry.

The war had only just begun.

Percy POV

After seeing Alex defeating the Goliath and sending the Brawlers after Kronos, then Kronos calling out a war cry, I knew the war had only just begun.

**(I thought about stopping here, but you guys deserve something more from my absence.)**

Annabeth POV**(Ha)**

After seeing Percy so heroic and crap. I thought about something that had been bothering me for about a year or two. Do I really love him?

Then I heard the war starting. I looked up to see Percy and Alex working together to push the strongest of the monsters back to the bridges entering Manhattan. They looked, oh how do I say this? I guess they looked "sexy".**(Just for your info I'm a boy and I am not gay, I just thought it would be a little bit funny to put that in there.) **They looked like a team. A team that works together.

I remembered to the day before when I yelled at Percy over Rachel. It was just a skirmish, but I made it bigger that it should've been. It should have been like a flower in the summer, so calm and nothing bothering it.

I just wish…Oh no.

**(Hell yea this is where it gets gory. Very bloody and gory indeed.) **

Alex POV

I think Annabeth was just stabbed.

I looked over to see Annabeth lying on the ground clutching her shoulder in pain. I ran as fast as I could over to her. I bent down to see green liquid flowing out of her shoulder with a purple taint mixed with it. On her left leg I saw a gash so deep that it went right to the bone and the bone was pulsing almost like the heart. It was very weird. On the other leg I saw her foot was almost cut off. I wanted to puke. Her bone was sticking out of her left leg like a spear.

Well I found the source of the pulsing. It was a parasite eating her bone. The thing was the size of my blade. It had demon red eyes, a rattlesnake tail, a big… never mind about that one, and three tropical centipedes living on its stomach, but the worst part was its teeth. Those were the size of my claws! I ripped the thing in half and stomped it on the ground as hard as I could. I could hear it wail in pain as I stomped on it.

I looked to find Percy, but he was nowhere in sight. I did a full 360 and didn't see him anywhere. I went to find Thaila and what I found was… different. I saw Percy holding a hurting Thaila.

"PERCY!" I yelled at him.

He turned around slowly and said, "Alex stop she needs to rest."

'THERE IS NO FUCKING TIME FOR YOUR SHIT, ANNABETH IS NEARLY DEAD!"

He got up quickly and followed me to Annabeth's tent that I put her in.

"She looks horrible, I'm going to throw up." He said.

"No you're not, come here." I hoisted him off the ground, "We are going to fix her are selves even if it kills us."

After about three hours of us trying to fix her up we got all of her bones and organs back into place. She still looked like hell, but at least we helped a little.

Three Hours Later, Alex POV

It just turned night as I came out of the central command. I turned the corner to see Kronos and Hyperion, the Titan of sunlight, walking around the city. I disguised myself as one of Kronos' minions.

Kronos turned to me and said, "How's the search for the young assface, Perseus Jackson?"

I replied, "The search has left me to nowhere, sir."

He looked at me really coldly and said, "I thought you were the best scavenger I had, I knew I should have killed you then and there."

He took Hyperion's spear and gutted me with it. I fell to the ground pretending to be dead. He and Hyperion started walking away. I got back to my regular feet, still in monster form, and started walking after them. I tapped Hyperion on the shoulder and he turned around.

He had the most surprising look on his face and he turned Kronos around. They looked at me in surprise.

I said, "You know it's too easy to find out who I really am." Then I changed back into my Alex form, and punched them both back into a wall. Kronos ran back to his camp back across the Brooklyn Bridge. Wimp. I turned to Hyperion who was just getting out of the rubble that I made. Then I thrust my hand out at him.**(Warning, Chronicle reference,AKA telekinesis powers.)**Then I saw him fly out of the rubble and stop right in front of me.

I started to close my hand into a fist. Hyperion started to wail out in pain. I kept closing my hand until it became a fist. When it became a fist I opened my hand as far out as I could open it and I pulled all of Hyperion's limbs off. He then lied there on the ground, dead with his legs and arms spread out on the ground around him.

I turned to the Brooklyn Bridge and Said to myself, "If they want a fight, I'll give em' a fight!"

**H.O.L.Y S.H.I.T I can't believe I did that in so little time!:D:D:D:D:D:D:D:D D:**

**I will try my hardest to make another chapter soon, I promise.**


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